6-N-(N-Methylanthranylamido)-4-Oxo-Hexanoic Acid: A New Fluorescent Protecting Group Applicable To A New Dna Sequencing Method

A General Synthetic Route to Isomeric Pyrrolo[1,2- x][1,4]diazepinones

A simple one-pot method for the synthesis of isomeric pyrrolo[1,2- x][1,4]diazepinones in reasonable yields was developed. The method is based on the condensation of readily available N-Boc amino acids with biomass-derived furans containing aminoalkyl groups followed by deprotection, furan ring opening, and Paal-Knorr cyclization. Using this approach, we synthesized pyrrolo[1,2- a][1,4]diazepin-3(2 H)-ones from furfurylamines and β-amino acids and pyrrolo[1,2- d][1,4]diazepin-4(5 H)-ones from 2-(2-furyl)ethylamines and α-amino acids. The cytotoxicity of the synthesized pyrrolodiazepinones was studied.

Nucleotides part LXXX: Synthesis of 3'-O fluorescence labeled thymidine derivatives and their 5'-O-triphosphates

A new labeling technique attaching a fluorescent pteridine derivative (3, 5) via a linker onto the 3'-OH group of 5'-O-dimethoxytritylthymidine (7) was developed to lead to the conjugates 8 and 11. After detritylation to give 9 and 12, the final conversion into the corresponding 5'-triphosphates (13, 14), which were isolated as sodium salts, was performed by known methods.

The removal of fluorescence in sequencing-by-synthesis

Fluorescent oligonucleotides provide useful way to study DNA during the sequencing-by-synthesis process. They allow researchers to determine the sequence of a short DNA strand. Fluorescence created by these chemicals must be removed after a few based pairs are read in order to continue reading the DNA sequence. Researchers have developed a variety of methods to solve this problem. This paper reviews the development of fluorescence removal in DNA sequencing and summarizes several methods of removing the fluorescence.

A new class of cleavable fluorescent nucleotides: synthesis and optimization as reversible terminators for DNA sequencing by synthesis

Fluorescent 2′-deoxynucleotides containing a protecting group at the 3′-O-position are reversible terminators enabling array-based DNA sequencing by synthesis (SBS) approaches. Herein, we describe the synthesis of a new family of 3′-OH unprotected cleavable fluorescent 2′-deoxynucleotides and their evaluation as reversible terminators for high-throughput DNA SBS strategies. In this first version, all four modified nucleotides bearing a cleavable disulfide Alexa Fluor® 594 dye were assayed for their ability to act as a reversible stop for the incorporation of the next labeled base. Their use in SBS leaded to a signal–no signal output after successive addition of each labeled nucleotide during the sequencing process (binary read-out). Solid-phase immobilized synthetic DNA target sequences were used to optimize the method that has been applied to DNA polymerized colonies or clusters obtained by in situ solid-phase amplification of fragments of genomic DNA templates.

Structure-based de novo design of ligands using a three-dimensional model of the insulin receptor

For the first time, a three-dimensional model of the insulin receptor is used in the de novo design of novel ligands that potentially mimic interactions of insulin at its receptor. Compound 4 competed with insulin as seen in autophosphorylation assays and inhibited up to 68% of IR autophosphorylation at 300 microM of 4 in 3T3IR cells induced by 1 nM insulin. This model provides a basis for the design of potent insulin receptor ligands.

Highly potent inhibitors of TNF-alpha production. Part II: metabolic stabilization of a newly found chemical lead and conformational analysis of an active diastereoisomer

Design and synthesis of metabolically stabilized inhibitors of TNF-alpha production, which could be new drug candidates, are reported. Conformational analysis of an active diastereoisomer was performed based on biological evaluations of the conformationally fixed indane derivatives 17 and 18. Structure-activity relationships (SARs) based on biological evaluations of the optically active derivatives are also discussed. Full details including chemistry are reported.

Highly potent inhibitors of TNF-alpha production. Part I: discovery of new chemical leads and their structure-activity relationships

Discovery of new chemical leads of inhibitors for TNF-alpha production starting from the chemical modification of 1 is reported. Further biological studies of 1 to disclose the site of its action strongly suggested that 1 inhibits LPS-induced TNF-alpha expression in the liver and spleen of mice. Structure-activity relationships (SARs) are also discussed and full details including the chemistry are reported.